I've noticed that over time there have been different rules for time travel. For example, originally the grandfather paradox was dealt with by the grandson either disappearing from the timeline or some other paradox set up. Now days, it seems more and more stories are using alternate timelines (like in Terra Nova). (And in the grandfather paradox stories, I don't think I ever saw one where, after the grandson disappeared, he wasn't there to cause the paradox, so he re-appeared only to disappear, then reappear in a loop.)

While every author or movie or TV show may have different rules, some seem to be standardized.

I've noticed one of these rules is conflicting memories. For example, when Marty McFly goes back in time and changes his present, he comes back, but remembers things as they were before he left -- he does not have memories of the changed events everyone else experienced. And, of course, those who didn't go back have only the memories of the new path and don't remember what Marty remembers. (I have yet to see Back to the Future II so I hope I'm not omitting anything.)

In Star Trek, with multiple time travel stories, people either remember the changed timeline or the original, but not both.

Is this rule ever broken? Are there stories where people have conflicting memories of an original and a changed timeline at the same time?

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Star Trek follows a great deal of different rules for time travel, depending on what the plot is going for. Often lampshaded with the oft-repeated phrase, "I hate temporal mechanics!"
– IzkataDec 28 '11 at 7:10

9 Answers
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The main character in the movie The Butterfly Effect receives the new set of memories on top of his original ones each time he completes a time jump. The accumulated knowledge leads to nosebleeds and eventually brain damage.

Likewise in the movie Frequency, the main character retains both sets of memories, but there is no apparent damage to his mind (beyond extreme confusion when it first happens).

Edit for Star Trek additions:

TNG 3x15, Yesterday's Enterprise - Guinan can sense when the timeline is wrong, to the point of being sure one of the Enterprise crew was supposed to be dead. Not actual memories, however.

TNG 7x25/26, All Good Things... - Picard was catapulted between three time periods in an alternate timeline by Q, and retained his memory of the events.

DS9 3x17, Visionary - Miles O'Brien experiences multiple jumps into the near future, seeing disasters that eventually get averted due to knowledge gained in these jumps. He would have remembered all these alternate futures, had he not died and sent a future version of himself (that didn't experience the jumps) back in time to complete the mission.

DS9 4x03, The Visitor - Benjamin Sisko experiences pieces of the far future, before being slingshot back to his correct time. He retains memories of that future, since he knew what to do to not get temporally displaced again.

VOY 3x21, Before and After - Kes is sent backwards through time from her death, and remembers the future, and warns the captain about the Krenim.

ENT 2x16, Future Tense - Trip, Reed, and Archer experience time loops, except they do retain their memories of each loop.

yes, I exactly thought about The Butterfly Effect when I read the question. But I presume both movies did not handle the concept realistically enough. Since memories are formed via neuro pathways, having a sudden burst of new "memories" would probably (and logically) cause seizure, or cause so much trauma that the individual would most likely fall into a coma. In any case, Back to the Future, in respect to it's cultural grandeur, is a 80's Hollywood production after all, so do not expect too much realism there. In such an area of mystery, the science fiction writer is free to guess.
– Yanick RochonDec 28 '11 at 7:24

River fails to shoot The Doctor, as she must since his "death" is a fixed point in time.

Amy, thanks to having grown up with a crack in her wall, still has memories of events from the original timeline, although they are fuzzy and incomplete.

The Series 5 story arc involves a timeline that is constantly changing due to

people, things, and events being erased from time completely by the cracks.

The Doctor, and eventually Amy, are able to remember things as they were in the original timeline. Likewise, when the original timeline is ultimately restored, the main characters (The Doctor, Amy, Rory, and presumably River) still have memories of events that occurred in the altered timeline.

Quantum Leap had a few episodes like that. One in particular was the JFK one. Where Al tells Sam that he prevented the death of Jackie? And that she was killed the first time around? I hated that episode because it seemed like such a weird ending.

Unless I'm remembering it wrong? Maybe I'm having a case of conflicting memories RIGHT NOW.

In Newton's Wake, time machines simply fail to operate if a contradiction would be caused. Although in this case the time machine is normally a ship's FTL drive, and they refer to the manoeuvre of trapping an enemy ship in its own light-cone (where it cannot jump without creating a paradox, so the jump drives fail) as a standard combat tactic.

I assume this is supposed to happen in a similar fashion to evanescent light waves which should be totally internally reflecting if refraction would remain inside the object.

This means that no-one has any memories of the aborted time-line, since it never happened. Or the time travel did happen, but in that case it always happened that way, so there is no conflict.

Roland, the main character, in a desolate post-apocalyptic future (sort of), has set up a paradox by saving Jake in 1977. As a result of which, he never meets Jake. So he remembers meeting Jake in the desert, and he also remembers passing through the desert alone and never meeting Jake. This is driving him mad.

In 1977, Jake also has what you call "conflicting memories". To put it mildly .. in his case, he remembers being killed!

Resolving this paradox was a major plot point for the third book (my favourite).

One thing to remember is that the real scientific understanding of time and the nature of our travel through it develops too. So the idea of alternate timelines comes out of developments in physics, indicating that this may be the way that real-life happens. Although without the crossovers.

Memories - I think we often tend to rationalise our memories, to make them a single timeline. Irrespective of what the "truth" is.

In the story, Senator Proxmire funds a time machine for the purposes of assaulting a young Robert Heinlein with a syringe full of antibiotics, thus curing Mr. Heinlein's incipient tuberculosis. The rest of the story revolves around the Law of Unintended Consequences...

Senator Proximire goes back in time and is successful in his assault. He winds up back with our time machine inventor, who then struggles with two sets of equally valid memories: one where Mr. Heinlein becomes an author and a time machine was built, the other where Admiral Heinlein becomes the Chief of Naval Operations and a policy maker with respect to the Russians, and no time machine. The story closes with Senator Proxmire learning exactly how much his actions hurt his own goals.

There was an episode of Outer Limits (the 1990s productions) titled "A Stitch in Time". Dr. Theresa Givens played by Amanda Plummer invents a time machine which she uses to travel back in time in order to kill rapists before they commit their crimes. Each time she returns to the present, she has to integrate memories of the newly altered timeline with her pre-existing memories. The alternate pasts progressively layer up in her mind, assaulting her sanity - somewhat like "The Butterfly Effect". I won't spoil the ending in case someone wants to watch the episode.